Alignments for a candidate for iorAB in Chromobacterium vaccinii MWU205

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Chromobacterium vaccinii MWU205

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate WP_046158511.1 VL52_RS19015 indolepyruvate ferredoxin oxidoreductase family protein

Query= reanno::Marino:GFF880
         (1172 letters)



>NCBI__GCF_000971335.1:WP_046158511.1
          Length = 1161

 Score = 1104 bits (2855), Expect = 0.0
 Identities = 565/1148 (49%), Positives = 776/1148 (67%), Gaps = 23/1148 (2%)

Query: 13   LEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQALWQA 72
            LE++Y   +G+V +TG QALVR+P++Q  LDR  GLNTAG V+GYRGSPLG VDQ + +A
Sbjct: 8    LEEKYTAPTGQVLMTGIQALVRLPMLQQELDRAAGLNTAGYVTGYRGSPLGNVDQTMIKA 67

Query: 73   KDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRAGDALK 132
            K  LD + + F P +NEDLAAT + GTQQV   E  + +GV+ LWYGKGPGVDR+GD LK
Sbjct: 68   KKHLDAHNVVFHPGLNEDLAATAVWGTQQVNIFEGAKYDGVYSLWYGKGPGVDRSGDVLK 127

Query: 133  HGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEFGLWGY 192
            HG   G+S HGGVL+V GDDH   SS+ PHQSD    +  +P ++P+ + E L+ GL G+
Sbjct: 128  HGNAAGTSKHGGVLLVCGDDHAAKSSTFPHQSDHILAASMIPVLSPSGVQEVLDLGLHGW 187

Query: 193  ALSRYSGCWVGFKAISETVESAASVEIPPAP-DFVTPDDFTAPESGLHYRWPDLPGPQLE 251
            A+SRYSGCWV  KAI++TVES+A V+I P   +F  P DF  PE GL+ RWPD P  Q +
Sbjct: 188  AMSRYSGCWVSIKAITDTVESSAIVDITPERLEFKIPKDFPLPEDGLNIRWPDTPLAQEK 247

Query: 252  TRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGIDEDKARDM 311
              + H+L A  A+AR N+++R   D+ + R GI+T GK +LD+++ALD LGI E +A D+
Sbjct: 248  RVLHHRLYAALAYARENKLNRITLDSPKPRLGIITCGKSYLDVMQALDDLGISEAQAADI 307

Query: 312  GLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYM---SEPDRPGEVLI 368
            GL I+KVGMVWPLE  G+  F  G EE+LV+EEKR IIE Q+KE +    +  RP  V  
Sbjct: 308  GLRIFKVGMVWPLEPEGVRQFAQGLEEILVVEEKRQIIEYQLKEQLYNWRDDIRPRVVGK 367

Query: 369  TGKQDELGRP----LIPYVGELSPKLVAGFLAARLGRFFE---VDFSERMAEISAMTTAQ 421
              ++ E   P    L+P  GEL+P ++A  +A RL   F+   +    +  +       Q
Sbjct: 368  FAEKGEWALPHGDWLLPAAGELTPAMIARAIANRLALIFDSPVIHDRLKFYDDKEAQLVQ 427

Query: 422  DPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMG-RNTESLIQMGGEGVNW 480
                + R+P++CSGCPHNTSTK+PEGS+A+AGIGCH+MA W+   NT++  QMGGEG+ W
Sbjct: 428  PRESIARVPHYCSGCPHNTSTKLPEGSRAVAGIGCHYMAHWISPENTKTFTQMGGEGITW 487

Query: 481  IGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDAVAMTGGQPVDGQ 540
            +G++ +T   H+F NLG+GTYFHSG +AIR AVA  +NITYKIL+NDAVAMTGGQ VDG 
Sbjct: 488  LGQAPFTTTRHIFTNLGDGTYFHSGILAIRAAVAGKVNITYKILYNDAVAMTGGQHVDGY 547

Query: 541  ITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELDQVQRELRDIPGC 600
            + V  + +Q+AAEGV R+V+ SD+P+KY     L P    FH R ELD+VQRELRDI G 
Sbjct: 548  LDVPMMTRQLAAEGVKRIVITSDDPDKYQNAQGLAPGIDVFH-RRELDRVQRELRDIEGV 606

Query: 601  TVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNCLSVVPRKTELGR 660
            T+LI+DQTCAAEKRRRRKR +FPDPAKRAFIN  VCEGCGDCS +S CLSV+P +T LGR
Sbjct: 607  TILIHDQTCAAEKRRRRKRNEFPDPAKRAFINERVCEGCGDCSKKSGCLSVLPVETPLGR 666

Query: 661  KRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLADIPAPKLPEMTG 720
            KRKIDQSSCNKD+SCV GFCPSFVT+EGG+LRK  G    S    K+  +P PK+P +  
Sbjct: 667  KRKIDQSSCNKDYSCVEGFCPSFVTVEGGKLRKPAG---ASADLAKMPALPMPKIPALHE 723

Query: 721  SYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVLSYVRMAPSPDKL 780
             + ++V GVGGTGVVT+GQ++ MAA+L+++G +VLD  G AQKGG+V S+VR+A S DKL
Sbjct: 724  PFGIMVTGVGGTGVVTIGQVLGMAAYLDNKGVTVLDMAGLAQKGGSVWSHVRIADSQDKL 783

Query: 781  HQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTADYVLFRDADMKAD 840
            H VRI+ G A+ V+ CDLVV ++++AL+ +R   +  + N  E PT+ ++   D    A 
Sbjct: 784  HAVRIAAGDANLVLGCDLVVTAAEEALAKMRDGFSHAIVNSYESPTSGFLKNPDIRYPAK 843

Query: 841  KRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLLPLSEAALMKAIE 900
                 +  AVG   F +++AN +A  LMGD + +N+ MLG+ WQKGL+P+S  A+M+A+ 
Sbjct: 844  AMKDAIVEAVGAGRFSEVNANKLATALMGDAIAANMFMLGYGWQKGLVPVSLEAIMEAVR 903

Query: 901  LNGVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVKPEPTLDELINTRHKHLVNY 960
            LNG A+  N++AF WGR +A D + V  L+  S   VV+  P  T D +++ R   L  Y
Sbjct: 904  LNGAAVKFNQDAFTWGRHAAQDLARVEALV--SPTAVVQFVPRETPDAVVHHRSTLLAAY 961

Query: 961  QNQRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQLYRFMAYKDEYEVARLFAETDFM 1020
            QN   A++Y+  V  VR+AEE+    +  LT A A+  +  +AYKDEYEVARL+++ +F 
Sbjct: 962  QNGALAERYKALVQQVRQAEEAAQPGSTALTLAAARAYHHLLAYKDEYEVARLYSDGEFQ 1021

Query: 1021 KEVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFGPWMFRAFRLLAKLRGLRGTAID 1080
            +EV   F+GD+K+ FH+    L+     +G+P+K   G W+  A ++LAKLR LRGTA+D
Sbjct: 1022 REVAAQFDGDYKLRFHIGVAWLT-----RGQPRKIAIGSWLMPAMKVLAKLRFLRGTALD 1076

Query: 1081 PFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLAELPADVRGYGPVREQAAES 1140
            PF +  DRKL+R ++ +++  +  +  +L        ++  +    VRG+G ++      
Sbjct: 1077 PFAWQDDRKLERQLIAEFEQELPALLAKLTPDTLPRAVEWMKTWEGVRGFGHIKLANYRQ 1136

Query: 1141 IREKQTQL 1148
             + +Q +L
Sbjct: 1137 AKTRQAEL 1144


Lambda     K      H
   0.319    0.136    0.405 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 3087
Number of extensions: 152
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1172
Length of database: 1161
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1114
Effective search space:  1253250
Effective search space used:  1253250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources